1998 Lincoln Town Car Not Charging (New alternator, good battery)

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I have a 1998 lincoln town car and it is not charging when running. Below is what I have done/tested.

replaced alternator with a reman from rockauto. After replacing and still experiencing the same problem I took the reman alternator to autozone and it tested good.

battery tested good.

the 2 wire plug on the back of the alternator broke during alternator replacement. I ordered a new pigtail and soldered the wires to the existing harness, correctly matching the old plug

using a test light with the key off, one of the pigtail wires is hot; when I start the car the other wire also turns on

the charging system fuse (number 13 under the hood) was blown. It was replaced. Of note, I drove the car for 2 years with the battery light on and never had any trouble.

the battery light on the dash comes on when keying on, after replacing the fuse 13 it goes out once the car is started

I can start the car without the pigtail plugged in. When plugging in the pigtail while running I can hear the alternator pull down. If I apply a load to the battery via a battery tester, while the car is running, I can hear the alternator pull down even further.

with the car running I used a voltmeter to test voltage at the back of the alternator and found it equal to what I was seeing at the battery (12.6v)

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How steady is the voltage reading on your voltmeter? I had the same issue and it was because the voltage wasn't constant because the remanufactured alternators weren't actually good. See my thread here: 06 TC: charging system light

Those would be the normal results if all is well. Also the battery warning light would be off with key off, on with key on but engine not running, off with engine running.

Since you have the battery warning light out when engine is running but only 12.6 volts instead of 14.x volts you may have a fried fusible link in the heavy circuit from the battery to the B+ connection on the alternator; or the alternator connections are not well connected, or corroded or damaged. The other option of the alternator or its regulator not working correctly has been discounted by the shop testing the "new" component as working.

The most usual cause of the fusible link getting damaged is the battery being connected with reverse polarity. The normally smooth fusible link will be burned and melted and twisted. But it will still carry a charge, just not enough for the alternator.

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